Contacts of the strand formed by residues 73 - 78 (chain J) in PDB entry 1VCB


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ALA 73 (chain J).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      4J  PHE      2.8     6.9    +      -       -      -
      5J  LEU*     3.3    12.1    -      -       +      +
      6J  MET*     2.8    26.8    +      -       -      +
     62J  PHE*     3.6    31.4    -      -       +      -
     66J  THR*     3.8    23.3    -      -       +      +
     67J  ALA*     3.8     6.9    -      -       +      +
     71J  ALA      3.8     1.0    +      -       -      -
     72J  PRO*     1.3    72.5    -      -       -      +
     74J  THR*     1.3    61.2    +      -       -      +
----------------------------------------------------------
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Residues in contact with THR 74 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      6J  MET*     3.4    32.5    -      -       -      +
      8J  ARG*     3.9    25.3    +      -       +      +
     45J  TYR      4.5     1.9    -      -       -      +
     46J  LYS*     4.8     7.6    -      -       -      +
     47J  ASP*     5.4     2.6    +      -       -      +
     62J  PHE*     4.0     9.5    -      -       -      -
     72J  PRO      3.9     1.4    +      -       -      -
     73J  ALA*     1.3    72.7    -      -       -      +
     75J  VAL*     1.3    72.6    +      -       -      +
     76J  GLY      4.3     1.2    +      -       -      +
     90J  ILE*     4.7    10.3    -      -       +      -
----------------------------------------------------------
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Residues in contact with VAL 75 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      5J  LEU*     4.3    24.7    -      -       +      -
      6J  MET      3.1     6.5    +      -       -      -
      7J  ILE*     3.4    14.9    -      -       +      +
      8J  ARG*     2.6    33.8    +      -       -      +
     27J  LEU*     4.6     8.1    -      -       +      -
     44J  LEU*     4.1    25.4    -      -       +      -
     45J  TYR      3.4    12.8    -      -       -      +
     51J  LEU*     4.8     3.1    -      -       +      -
     62J  PHE*     3.6    31.6    -      -       +      -
     74J  THR*     1.3    77.2    -      -       -      +
     76J  GLY*     1.3    71.9    +      -       -      +
----------------------------------------------------------
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Residues in contact with GLY 76 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      8J  ARG      3.5     5.6    -      -       -      -
     44J  LEU*     3.3     8.3    -      -       -      +
     45J  TYR*     2.9    40.0    +      -       -      -
     46J  LYS*     5.1     0.6    -      -       -      +
     47J  ASP      5.6     1.0    -      -       -      +
     74J  THR*     4.2     2.0    -      -       -      +
     75J  VAL*     1.3    79.0    -      -       -      +
     77J  LEU*     1.3    59.4    +      -       -      -
     88J  LEU*     3.8    16.8    -      -       -      -
     90J  ILE*     4.1     9.6    -      -       -      -
----------------------------------------------------------
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Residues in contact with LEU 77 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      7J  ILE*     4.3    15.7    -      -       +      +
      8J  ARG      2.9    10.3    +      -       -      +
      9J  ARG*     3.4    38.6    -      -       +      +
     14J  ILE*     5.9     0.2    -      -       +      -
     31J  VAL*     4.0     8.7    -      -       +      -
     35J  LEU*     3.8    29.2    -      -       +      -
     42J  GLN*     3.7    27.4    -      -       +      +
     43J  ARG      3.4     6.3    -      -       -      +
     44J  LEU*     3.3    23.6    -      -       +      -
     45J  TYR*     4.8     0.2    -      -       -      -
     76J  GLY*     1.3    75.1    -      -       -      +
     78J  ALA*     1.3    66.4    +      -       -      +
     79J  PHE*     3.9    12.8    -      -       +      -
     86J  GLU*     4.5     0.7    -      -       -      +
     88J  LEU*     3.2    17.1    -      -       -      +
     89J  CYS      4.8     1.4    +      -       -      -
----------------------------------------------------------
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Residues in contact with ALA 78 (chain J). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
      9J  ARG*     4.6     0.2    -      -       -      +
     41J  GLU      3.8     0.2    -      -       -      +
     42J  GLN*     3.4     5.7    -      -       -      +
     43J  ARG*     3.0    37.0    +      -       +      +
     45J  TYR*     3.7    26.5    -      -       +      +
     77J  LEU*     1.3    76.6    -      -       -      +
     79J  PHE*     1.3    63.9    -      -       -      +
     85J  PHE*     5.5     0.6    -      -       +      +
     86J  GLU*     3.8    28.7    -      -       +      +
     88J  LEU*     4.5     8.5    -      -       -      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il